Merge branch 'dev' into fix/electrodegroup_position

NeurodataWithoutBorders · Sep 5, 2024 · 3b2bf9f · 3b2bf9f
2 parents 4837aba + aaa4d65
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,9 @@
 
 ## PyNWB 2.8.2 (Upcoming)
 
+### Enhancements and minor changes
+- Added support for numpy 2.0. @mavaylon1 [#1956](https://github.com/NeurodataWithoutBorders/pynwb/pull/1956)
+
 ### Documentation and tutorial enhancements
 - Added pre-release pull request instructions to release process documentation @stephprince [#1928](https://github.com/NeurodataWithoutBorders/pynwb/pull/1928)
 - Added section on how to use the `family` driver in `h5py` for splitting data across multiple files @oruebel [#1949](https://github.com/NeurodataWithoutBorders/pynwb/pull/1949)

diff --git a/docs/source/export.rst b/docs/source/export.rst
@@ -53,14 +53,12 @@ on the :py:class:`~pynwb.file.NWBFile` before exporting.
 
 How do I create a copy of an NWB file with different data layouts (e.g., applying compression)?
 ---------------------------------------------------------------------------------------------------------
-Use the `h5repack <https://support.hdfgroup.org/HDF5/doc/RM/Tools.html#Tools-Repack>`_ command line tool from the HDF5 Group.
-See also this `h5repack tutorial <https://support.hdfgroup.org/HDF5/Tutor/cmdtooledit.html#chglayout>`_.
+Use the `h5repack <https://docs.hdfgroup.org/hdf5/v1_14/_view_tools_edit.html>`_ command line tool from the HDF5 Group.
 
 
 How do I create a copy of an NWB file with different controls over how links are treated and whether copies are deep or shallow?
 ---------------------------------------------------------------------------------------------------------------------------------
-Use the `h5copy <https://support.hdfgroup.org/HDF5/doc/RM/Tools.html#Tools-Copy>`_ command line tool from the HDF5 Group.
-See also this `h5copy tutorial <https://support.hdfgroup.org/HDF5/Tutor/cmdtooledit.html#copy>`_.
+Use the `h5copy <https://docs.hdfgroup.org/hdf5/v1_14/_view_tools_edit.html>`_ command line tool from the HDF5 Group.
 
 
 How do I generate new object IDs for a newly exported NWB file?
@@ -101,8 +99,8 @@ For example:
            export_io.export(src_io=read_io, nwbfile=nwbfile, write_args={'link_data': False})  # copy linked datasets
            # the written file will contain no links to external datasets
 
-You can also the `h5copy <https://support.hdfgroup.org/HDF5/doc/RM/Tools.html#Tools-Copy>`_ command line tool \
-from the HDF5 Group. See also this `h5copy tutorial <https://support.hdfgroup.org/HDF5/Tutor/cmdtooledit.html#copy>`_.
+You can also the `h5copy <https://docs.hdfgroup.org/hdf5/v1_14/_view_tools_edit.html>`_ command line tool \
+from the HDF5 Group.
 
 
 How do I write a newly instantiated ``NWBFile`` to two different file paths?

diff --git a/pyproject.toml b/pyproject.toml
@@ -34,8 +34,8 @@ classifiers = [
 ]
 dependencies = [
     "h5py>=2.10",
-    "hdmf>=3.14.0",
-    "numpy>=1.18, <2.0", # pin below 2.0 until HDMF supports numpy 2.0
+    "hdmf>=3.14.3",
+    "numpy>=1.18",
     "pandas>=1.1.5",
     "python-dateutil>=2.7.3",
 ]

diff --git a/requirements-min.txt b/requirements-min.txt
@@ -1,6 +1,6 @@
 # minimum versions of package dependencies for installing PyNWB
 h5py==2.10  # support for selection of datasets with list of indices added in 2.10
-hdmf==3.14.0
+hdmf==3.14.3
 numpy==1.18
 pandas==1.1.5
 python-dateutil==2.7.3
diff --git a/requirements.txt b/requirements.txt
@@ -1,6 +1,6 @@
 # pinned dependencies to reproduce an entire development environment to use PyNWB
 h5py==3.11.0
-hdmf==3.14.0
-numpy==1.26.4
+hdmf==3.14.3
+numpy==2.1.1
 pandas==2.2.2
 python-dateutil==2.9.0.post0